Contacts of the helix formed by residues 157 - 174 (chain D) in PDB entry 3HYW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 157 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ALA* 3.5 19.3 - - + -
154D VAL* 3.3 34.8 - - + -
155D SER* 4.0 4.7 + - - -
156D CSS 1.3 76.9 - - - -
158D GLY* 1.3 68.1 + - - +
159D PRO* 3.3 3.6 - - - -
160D ALA* 3.0 19.9 + - + +
161D TYR* 3.3 27.7 + + + -
184D PHE* 6.1 0.9 - + - -
186D THR* 3.5 17.9 - - - -
187D SER* 3.5 14.1 - - - -
188D GLU* 3.5 25.4 - - + +
194D PHE* 3.6 26.4 + - + -
195D GLY* 3.9 15.3 - - - -
251D MET* 5.1 0.2 - - - -
308D THR* 3.4 20.0 - - - -
309D GLY 4.3 0.2 - - - -
800D PS9 3.7 3.2 - - - -
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Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PHE* 1.3 76.4 - - - +
159D PRO* 1.3 61.7 - - - +
161D TYR* 3.1 12.6 + - - +
162D GLU* 2.9 31.1 + - - +
194D PHE* 4.5 10.5 - - - -
349D ALA* 4.8 8.0 - - - +
800D PS9 3.4 13.4 - - - -
802D PS9 4.4 5.2 - - - -
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Residues in contact with PRO 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PRO* 4.4 2.1 - - + +
123D ILE* 3.7 9.8 - - + +
156D CSS 4.0 13.5 - - - +
157D PHE 3.4 4.3 - - - -
158D GLY* 1.3 90.2 - - - +
160D ALA* 1.3 55.2 + - - +
162D GLU* 3.5 13.7 - - - +
163D PHE* 2.9 30.8 + - - +
251D MET* 4.3 11.4 - - - -
441D FAD 3.4 56.1 - - + +
800D PS9 3.8 12.1 - - - -
802D PS9 4.4 1.3 - - - -
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ILE* 3.7 8.1 - - + +
149D GLY 4.1 10.1 - - - +
150D ALA* 5.5 1.1 - - + -
157D PHE* 3.0 12.3 + - + +
159D PRO* 1.3 75.3 - - - +
161D TYR* 1.3 61.1 + - - +
163D PHE* 3.5 0.3 + - - +
164D ALA* 2.9 30.3 + - - +
184D PHE* 3.6 22.1 - - + -
249D MET* 4.1 10.8 - - - -
251D MET* 3.7 26.9 - - + +
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Residues in contact with TYR 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PHE* 3.3 24.9 + - + -
158D GLY* 3.1 7.5 + - - +
160D ALA* 1.3 74.1 - - - +
162D GLU* 1.3 66.2 + - - +
164D ALA* 3.3 2.5 + - - +
165D LEU* 3.0 36.6 + - + +
184D PHE* 3.5 29.0 - + - -
188D GLU* 2.6 37.1 + - - -
191D LEU* 3.4 10.6 - - + +
192D GLY 3.0 21.0 + - - -
194D PHE* 3.8 22.7 - + + -
206D VAL* 3.4 30.5 - - + -
210D PHE* 3.6 21.5 - + - -
349D ALA* 5.5 3.6 - - + -
351D PHE* 5.0 4.7 - - + -
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PRO 4.8 0.3 - - - +
46D PRO* 3.8 21.3 - - + +
47D HIS* 4.1 2.9 - - - -
158D GLY 2.9 13.7 + - - +
159D PRO* 3.5 13.0 - - - +
161D TYR* 1.3 78.5 - - - +
163D PHE* 1.3 57.0 + - - +
165D LEU* 3.4 0.7 + - - -
166D MET* 2.9 43.8 + - - +
348D ILE 3.6 1.2 - - - +
349D ALA* 4.0 7.6 - - + +
350D ASP* 2.7 55.8 + - - +
351D PHE* 4.6 6.4 - - - -
382D LYS* 3.2 22.9 + - - -
441D FAD 4.6 8.0 + - - -
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PRO* 4.3 10.7 - - + +
49D ALA* 4.0 19.1 - - + -
50D MET* 3.6 24.9 - - + -
123D ILE* 3.9 19.3 - - + -
132D THR* 4.0 13.5 - - + -
136D LEU* 3.9 21.5 - - + -
148D ILE* 3.7 18.4 - - + -
159D PRO 2.9 22.0 + - - +
160D ALA 3.8 3.6 - - - +
161D TYR 3.3 0.2 - - - -
162D GLU* 1.3 70.5 - - - +
164D ALA* 1.3 58.7 + - - +
166D MET* 3.7 6.8 - - - +
167D LEU* 2.9 35.8 + - + +
247D PHE* 3.9 14.4 - + - -
249D MET* 3.7 33.2 - - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ILE* 3.8 20.9 - - + -
160D ALA 2.9 18.5 + - - +
161D TYR* 3.6 5.8 - - - +
163D PHE* 1.3 77.3 - - - +
165D LEU* 1.3 58.7 + - - +
168D HIS* 3.0 24.8 + - - +
182D MET* 3.2 15.6 - - + +
184D PHE* 4.0 21.1 - - + -
210D PHE* 4.7 9.6 - - + -
215D ILE* 4.8 7.1 - - + +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D TYR* 3.0 31.6 + - + +
162D GLU 3.9 0.4 - - - +
164D ALA* 1.3 74.2 - - - +
166D MET* 1.3 60.3 + - - +
168D HIS* 3.5 6.6 + - + +
169D TYR* 3.0 23.0 + - - +
206D VAL* 5.8 0.4 - - + -
209D LEU* 4.4 9.9 - - + +
210D PHE* 3.6 35.4 - - + -
213D ARG* 3.9 32.0 - - + +
215D ILE* 4.5 12.3 - - + -
351D PHE* 3.2 57.5 - - + +
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Residues in contact with MET 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PRO* 3.4 24.9 - - - +
47D HIS* 3.5 26.7 - - + +
50D MET* 3.2 39.9 - - + +
52D TRP* 3.5 32.9 - - + -
162D GLU* 2.9 41.7 + - - +
163D PHE* 3.7 5.2 - - - +
165D LEU* 1.3 73.7 - - - +
167D LEU* 1.3 59.1 + - - +
169D TYR* 3.3 4.5 + - - +
170D GLU* 3.0 27.5 + - - +
350D ASP* 3.7 11.4 - - + +
351D PHE 3.7 11.0 - - - -
352D GLY 4.2 0.4 - - - +
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D MET* 3.8 12.9 - - + +
136D LEU* 3.7 31.9 - - + -
139D LEU* 4.6 2.0 - - + -
140D TYR* 4.0 12.1 - - + +
146D VAL* 3.8 33.7 - - + -
148D ILE* 3.9 11.0 - - + -
163D PHE* 2.9 24.2 + - + +
164D ALA 3.7 3.4 - - - +
166D MET* 1.3 74.5 - - - +
168D HIS* 1.3 60.0 + - - +
170D GLU* 3.1 1.3 + - + +
171D LEU* 2.9 59.8 + - + +
182D MET* 4.1 3.4 - - + -
247D PHE* 4.2 3.6 - - + -
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Residues in contact with HIS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B ARG 5.0 1.6 - - - -
368B GLU 4.8 4.7 - - - -
164D ALA 3.0 14.0 + - - +
165D LEU* 3.6 11.2 - - + +
167D LEU* 1.3 76.3 - - - +
169D TYR* 1.3 66.2 + - + +
171D LEU* 3.4 4.3 + - - +
172D LYS* 3.1 58.5 + - + +
177D ARG* 2.9 29.9 + - + -
182D MET* 3.9 16.7 - - - +
213D ARG* 3.3 59.4 + - + +
215D ILE* 4.0 5.6 - - + -
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Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D TRP* 3.6 30.1 - + - -
165D LEU 3.0 14.3 + - - +
166D MET 3.3 7.6 - - - +
167D LEU 3.2 0.2 - - - -
168D HIS* 1.3 83.4 - - + +
170D GLU* 1.3 62.3 + - - +
172D LYS* 3.5 6.7 + - + +
173D LYS* 2.7 70.6 + - + +
351D PHE 3.7 9.0 - - - +
352D GLY* 4.1 6.7 - - - -
353D GLU* 4.0 46.9 - - + +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D MET* 3.4 25.6 - - + -
52D TRP* 3.1 29.5 + - + -
140D TYR* 3.3 24.9 - - + +
166D MET 3.0 6.2 + - - +
167D LEU* 3.1 4.7 + - + +
169D TYR* 1.3 79.1 - - - +
171D LEU* 1.3 62.1 + - - +
173D LYS* 3.3 8.2 + - - +
174D ARG* 2.9 66.3 + - - +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 4.8 6.1 - - + -
140D TYR* 3.7 24.0 - - + -
146D VAL* 5.2 0.2 - - + -
167D LEU* 2.9 46.0 + - + +
168D HIS 3.7 4.0 - - - +
170D GLU* 1.3 76.1 - - - +
172D LYS* 1.3 59.2 + - - +
174D ARG* 3.3 1.8 + - - -
175D GLY 2.9 7.6 + - - -
176D ILE* 2.8 39.8 + - + +
177D ARG* 3.9 17.7 - - + +
180D VAL* 3.7 36.6 - - + -
182D MET* 3.9 22.2 - - + -
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B GLU* 3.2 37.3 + - - +
369B ARG* 4.3 5.1 - - - +
431B SO4 2.9 43.1 + - - -
168D HIS* 3.1 47.3 + - + +
169D TYR* 3.7 7.0 - - + +
171D LEU* 1.3 74.5 - - - +
173D LYS* 1.3 60.1 + - + +
175D GLY* 2.8 20.4 + - - -
177D ARG* 3.8 18.2 - - + -
213D ARG* 6.1 0.4 - - - +
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D TYR* 2.7 69.0 + - + +
170D GLU* 3.3 11.0 + - - +
172D LYS* 1.3 76.8 - - + +
174D ARG* 1.3 62.0 + - + +
175D GLY 3.5 0.2 + - - -
353D GLU* 5.2 3.0 + - - -
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Residues in contact with ARG 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN* 3.9 15.6 + - - +
140D TYR* 3.5 59.7 - - - +
170D GLU* 2.9 44.9 + - - +
171D LEU 3.8 4.7 - - - +
172D LYS 3.1 0.4 - - - -
173D LYS* 1.3 77.0 - - + +
175D GLY* 1.3 61.3 + - - +
176D ILE* 3.4 20.2 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il